xrayatten 0.1.1

YAML-driven local NIST v1.4 X-ray attenuation workflows

XrayAtten

YAML-driven X-ray attenuation workflows based on a packaged local NIST v1.4 coefficient snapshot.

Language: English | Chinese

Overview

xrayatten computes X-ray attenuation quantities for user-defined materials and layered stacks. Formal workflows use the bundled local NIST v1.4 snapshot; online NIST XCOM queries are available only as optional comparison outputs.

Release note: This update expands the coefficients workflow with selected energy-point output and bounded energy-range export. Range exports reuse the configured precision grid, preserve absorption-edge handling, and reject empty or invalid ranges, making batch attenuation and approximate energy-absorption tables easier to publish, compare, and reproduce across GitHub and PyPI releases.

The package currently supports:

• material coefficient tables for total attenuation and approximate energy absorption;
• primary-beam attenuation versus thickness at user-selected energies;
• first-collision absorbed-energy estimates versus thickness;
• cumulative primary-beam attenuation profiles through multilayer stacks.

Highlights

• YAML-first workflows for reproducible calculations.
• Packaged local data under src/xrayatten/data, including 92 element coefficient tables and SHA-256 manifest validation.
• One absorption-edge-aware log-log interpolation implementation shared by all workflows.
• Dense coefficient grids with selectable precision.
• Provenance metadata in every TXT output.
• Optional online NIST XCOM comparison for coefficient workflows.
• Developer tests for data integrity, interpolation, physics rules, YAML validation, and workflow outputs.

Installation

Python 3.10 or newer is required.

Install the released package:

python -m pip install xrayatten

Install optional online comparison support:

python -m pip install "xrayatten[online]"

Install from source for development:

python -m pip install -e ".[dev,online]"

If you only need local calculation from a source checkout:

python -m pip install -e .

Quick Start

Validate the bundled local NIST data:

xrayatten validate-data

Run an example workflow:

xrayatten run configs/examples/coefficients_batch.yaml

The module form is equivalent and useful before console scripts are on PATH:

python -m xrayatten validate-data
python -m xrayatten run configs/examples/coefficients_batch.yaml

Workflows

Workflow	Purpose	Energy policy
coefficients	Write material coefficient tables for total attenuation and approximate energy absorption	Uses the full precision grid by default; can use selected energies_kev points or an energy_range_kev precision-grid subset
attenuation_vs_thickness	Compute primary-beam transmission and attenuation versus thickness	Uses user-provided energies_kev
energy_absorption_vs_thickness	Estimate first-collision absorbed-energy fraction versus thickness	Uses user-provided energies_kev
multilayer_attenuation_profile	Compute cumulative primary-beam attenuation through fixed layers	Uses user-provided energies_kev

Example configuration:

schema_version: 1
workflow: coefficients
output_dir: results/my_coefficients
energies_kev: null
# Optional range mode; leave unset unless requesting a precision-grid subset.
# energy_range_kev:
#   start: 10
#   stop: 100
precision: low
online_comparison: false

materials:
  - id: blue_glass
    composition_basis: atomic_ratio
    composition:
      Si: 50
      B: 20
      Li: 20
      Mg: 10
      Y: 2
      Cs: 10
      Ce: 1
      O: 155
      F: 9
    density_g_cm3: 2.5
    density_source: project configuration

More runnable examples are available in configs/examples.

Calculation Model

Material composition can be provided as either:

• atomic_ratio: converted to mass fractions using elements.csv;
• mass_fraction: already normalized to exactly 1.

Material coefficients use mass-fraction additivity:

(mu/rho)_material = sum_i w_i * (mu/rho)_i
(mu_en/rho)_material ~= sum_i w_i * (mu_en/rho)_i

If density_g_cm3 is provided, linear coefficients are computed as:

mu = (mu/rho) * density

Thickness workflows then use:

T(x) = exp(-mu*x)
R(x) = 1 - T(x)
A_E(x) = (mu_en/mu) * (1 - exp(-mu*x))

A_E is a first-collision absorbed-energy estimate, not a full deposited-dose or detector-efficiency model.

Interpolation

All workflows use the same interpolation implementation.

1. Element tables are loaded from the local NIST v1.4 snapshot and checked against manifest SHA-256 values.
2. Energies are converted from MeV to keV for calculation and output.
3. Repeated energy rows are treated as absorption edges.
4. Full coefficient tables preserve both below and above edge rows.
5. Exact single-energy queries at an edge use the above value.
6. Non-edge points use piecewise log-log interpolation.
7. Interpolation never crosses an absorption edge and never extrapolates.
8. Non-finite interpolation results are rejected before output.

The coefficients workflow builds a dense grid from all original NIST energy points, all absorption-edge rows, and additional gap-fill points controlled by precision. With energy_range_kev, that same precision grid is filtered to the inclusive range; the range mode does not add arbitrary boundary points. With energies_kev, only the requested points are written.

precision	Relative density	Typical use
super	Highest	Archival high-resolution curves
high	High	Detailed plotting
medium	Medium	Balanced output size and smoothness
low	Default	Routine plotting and Origin import
fast	Lowest	Quick preview
direct	Original points only	NIST points and absorption-edge rows, without added grid points

Output

All TXT files include metadata header lines followed by tab-separated columns.

Coefficient outputs:

• attenuation: Energy_keV, Edge_side, Mass_mu_over_rho_cm2_g, and Linear_mu_cm_inverse when density is available;
• approximate energy absorption: Energy_keV, Edge_side, Mass_mu_en_over_rho_approx_cm2_g, and Linear_mu_en_approx_cm_inverse when density is available.

Thickness attenuation outputs:

• Thickness_cm
• Mass_mu_over_rho_cm2_g
• Linear_mu_cm_inverse
• Transmission_fraction
• Attenuation_fraction

First-collision energy-absorption outputs:

• Thickness_cm
• Transmission_fraction
• Attenuation_fraction
• First_collision_absorbed_energy_fraction
• Removed_not_absorbed_fraction

Multilayer outputs:

• Depth_from_incident_surface_cm
• Stack_coordinate_from_bottom_cm
• Layer_id
• Interface_position
• Cumulative_optical_depth
• Transmission_fraction
• Attenuation_fraction

Configuration Rules

Field	Rule
schema_version	Required; currently 1
workflow	One of coefficients, attenuation_vs_thickness, energy_absorption_vs_thickness, multilayer_attenuation_profile
output_dir	Required; absolute paths are used as-is, relative paths resolve from the current working directory
composition_basis	atomic_ratio or mass_fraction
density_g_cm3	Positive number, or null only for coefficients
energies_kev	null or a non-empty selected point list for coefficients; required for attenuation, energy-absorption, and multilayer workflows
energy_range_kev	Optional {start, stop} range for coefficients; mutually exclusive with a non-null energies_kev; uses the selected precision grid
precision	direct, super, high, medium, low, or fast; used only by coefficients
online_comparison	Optional for coefficients; supports atomic_ratio materials only

Important behavior:

• Configuration validation happens before output directories are created.
• Energies are limited to the supported local NIST range; extrapolation is rejected.
• If local coefficient outputs are written but online XCOM comparison fails, the error message explicitly says that local outputs were completed.

Project Layout

src/xrayatten/                 package source
src/xrayatten/data/            bundled NIST data and element metadata
configs/examples/              runnable YAML examples
docs/                          method, configuration, reproducibility, and migration notes
tests/                         developer test suite
pyproject.toml                 package metadata and optional dependencies

Testing

Tests are for developers, maintainers, CI, and source reviewers. They are not required for normal pip install xrayatten users.

python -m pytest -q
python -m pytest --cov=xrayatten --cov-report=term-missing

Validate local data:

python -m xrayatten validate-data

Syntax-check without writing __pycache__:

python -B -c "from pathlib import Path; files=list(Path('src').rglob('*.py'))+list(Path('tests').rglob('*.py')); [compile(p.read_text(encoding='utf-8'), str(p), 'exec') for p in files]"

Scientific Scope

This package computes monoenergetic narrow-beam attenuation using local NIST coefficient tables and deterministic formulas. It does not model scattered photon buildup, fluorescence escape or reabsorption, bremsstrahlung transport, or coupled photon-electron Monte Carlo transport.

Use docs/METHODS_VALIDATION.md when preparing publication text or method descriptions.

Documentation

Document	Description
README.zh-CN.md	Chinese README
docs/METHODS_VALIDATION.md	Scientific formulas, limitations, and validation notes
docs/CONFIGURATION.md	YAML configuration reference
docs/REPRODUCIBILITY.md	Data versioning, checksums, and output metadata
docs/MIGRATION.md	Migration notes from older scripts to YAML workflows